have you checked inside the distributer to see if the contacts/metals (whatever you call them) are properly spaced? long story short, was doing a tune up, messed with it and had miss fires. went to toyota sjc and they put it back in proper measurement.
It's one thing I'm going to have Jay check. I could check the gap on the NE pick up. Spec is .2mm to .4mm and it's at the lower side. I don't own a 30mm socket to move the crank pully to get the pick up coil around in the distributor to check the gaps at G1 and G2. Rotor is making good contact on all six points in the cap.
My uneducated (but learning) brain thinks it's one or both of those gaps and/or the timing.
Ignition coil resistence on both the primary and secondary coil check out just fine and the truck starts up great, so I've ruled out the ignition coil.
I've also ruled out the 'brittle wire syndrome' of the engine harness back by the EGR pipe because I move the hell out of that harness both there and at the ECU w/o any change to the engine misfire pattern. Based on that 'scientific' test, I don't think it's got anything to do with the harness.
I've put a can of BG44K fuel system cleaner thru so I don't think it's the injectors. Read on a thread or two that removing some of the hoses above the engine can result in a coolant spill that could clog the injectors.
Don't know what kind of plugs Hanlon put in (twice new now), but if they aren't Denso, will probably have Eric/Jay put OEM Denso plugs in. Ignition wires are new as of August/September '09 and we've tested all six of those and continuity is good on them too.
I don't know what else it could be but the distributor housing and/or timing at this point. Everything else has been theoretically ruled out as a cause. The dizzy housing by itself isn't that expensive. Shoot - CDAN even pointed out that the 4 components of the dizzy separately are less expensive than the whole. Go figure that one out.
I just hope master Jay can figure it out! I really like the truck as she's currently configured and don't really want a car payment for the next 5 years.

car will be paid off in November and my daily Miata next May I think. How often to many of us get to really celebrate NO car payments!
EDIT - just reread what you'd said - they were able to adjust the gaps in the housing? Hmmm...FSM says if those 3 gaps were not in spec to replace the distributor so figured if the gaps were buggered I'd have to spring for a new housing.
Stan - I need a truck prayer from you buddy.